Lost all my custom keyboard shortcuts
My guess is that you just upgraded Blender, and didn't click 'Copy Previous Settings' in the splash screen. This would copy your settings of 2.78 to 2.79; without this, Blender uses the defaults after an upgrade.

If you haven't saved new settings yet, the 'Copy Previous Settings' button will still be available in the splash screen. If you want to remove your 2.79 settings, you have to visit a platform-dependent path. These paths are documented in the Blender Manual.